docs: def extract(self, reads_to_extract, database_fasta_file, output_file):
          '''Extract the reads_to_extract from the database_fasta_file and put them in
          output_file.
  
          Parameters
          ----------
          reads_to_extract: Iterable of str
              IDs of reads to be extracted
          database_fasta_file: str
              path the fasta file that containing the reads
          output_file: str
              path to the file where they are put
  
          Returns
          -------
          Nothing'''
          cmd = "fxtract -XH -f /dev/stdin '%s' > %s" % (
              database_fasta_file, output_file)
  
          extern.run(cmd, stdin='\n'.join(reads_to_extract))